Tag Archives: C. difficile research community

Researchers At University of Texas Health Science Center and Graduate School of Biomedical Sciences in Houston Have Uncovered How C. difficile Produces the Toxins A and B That Are Responsible For Causing Disease


In the battle against drug-resistant pathogens, genetic research holds promising answers to our toughest threats. A new study shows that the best tool for
treating Clostridium difficile
infections could be within the genome of the bacteria itself.

Researchers at the University of Texas Health Science Center and the Graduate School of Biomedical Sciences in Houston have uncovered an important new finding to learn just how the C. difficile bacteria produces toxins, offering some new direction for the development of non-antibiotic drugs to fight dangerous C. difficile infections (CDI).

Strain on already stressed healthcare industry —–   The bacteria are one of the more virulent and widespread drug-resistant pathogens responsible for healthcare associated infections around the world, costing acute care facilities nearly $4.8 billion dollars a year in excess healthcare costs in the United States.

HOW is C. diff. Acquired?   —-   CDIs are linked to the use of broad spectrum antibiotics, which when used to treat infections can also suppress the beneficial bacteria that live in our guts and protect us from infections.   When that intestinal microflora is compromised, individuals become more susceptible to CDIs when exposed to C. difficile bacteria on contaminated surfaces or other individuals who are carrying the bacteria.

CDC Report —    C. difficile works by producing two toxins, toxin A and toxin B, that cause life-threatening diarrhea as well as pseudomembranous colitis, toxic megacolon, perforations in the colon, sepsis and — death. According to a 2015 study from the Centers for Disease Control and Prevention (CDC), there are nearly half a million CDIs in the United States each year, and about 15,000 of those cases result in deaths. The CDC considers C. difficile a public threat needing urgent and aggressive action.

The authors of the new study from the University of Texas have uncovered just how                 C. difficile produces the toxins A and B that are responsible for causing disease.

They studied several strains of the bacteria and found that some encode two Agr loci in their genomes, designated agr1 and agr2. The agr1 locus is present in all of the C. difficile strains sequenced to date, whereas the agr2 locus is present in a few strains.

Until recently, the function of these loci were not known. To understand their roles in toxin regulation and pathogenesis, the researchers used allelic exchange to delete components of agr1 and agr2 and then examined the mutants for toxin production. In their results, they found that the agr1 mutant cannot produce toxins A and B – in their model the mutant was able to colonize but could not produce disease.

These findings offer a potential new approach to treating CDIs for a global medical community vexed by the dangerous pathogen and in need of a novel solution.

“The toxins have become promising non-antibiotic treatment targets,” write the authors. “Here, we have identified a pathway responsible for activating the production of the toxins.

This important finding opens up a unique therapeutic target for the development of a novel non-antibiotic therapy for C. difficile infections.”

Study author Charles Darkoh, PhD, explains how his team plans on building on their research findings. “By crippling their toxin-making machinery, C. diff cannot make toxins and thus cannot cause disease. My laboratory is already working on this and was awarded a 5-year National Institutes of Health grant to investigate and develop an oral compound we have identified that inactivate the toxins and block the toxin-making machinery
of C. diff by targeting this pathway.”

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Researchers at MGGen Are Part Of a Community Study In Flagstaff, AZ On Two Serious Infection-Causing Bacteria; Clostridium difficile and Staphylococcus aureus



Researchers at Northern Arizona University’s Center for Microbial Genetics and Genomics, or MGGen, are putting out a call for poop.

The request is part of a community study on two nasty infection-causing bacteria in order to identify how the bugs are being carried around Flagstaff,  AZ and how they are making their way into the hospital.

The researchers say the pathogens could be present on any number of things, from dogs to ground meat to humans themselves.

It is hoped that confirming those reservoirs and tracking how the bacteria are transmitted will lead to new recommendations for how people and hospitals can better prevent the infections, the researchers said.


The two bacteria, Clostridium difficile, or C. diff, and Staphylococcus aureus, or Staph, are important to study because they are notorious for causing hospital-acquired infections that are often difficult to treat.

Staph can cause skin and respiratory infections while symptoms of C. diff infections include diarrhea and fever.

For the research project, MGGen scientists are comparing Staph and C. diff bacteria collected from sick patients at Flagstaff Medical Center to those bacteria carried by healthy people.

Samples of the latter come from volunteers willing to provide a swab from inside their nose and a swab of their fecal material from used toilet tissue. The researchers have received 65 healthy community member samples and their goal is to get 500 by next April.

MGGen’s specialty is whole genome sequencing, which allows scientists to compare even the tiniest genetic variations between the samples. With that, they can tell how closely the samples are related, indicating potential transmission paths.

The study has found:  that the bacteria strains in ill patients don’t match those found in other hospital cases, indicating the organisms aren’t lingering in the hospital and being transmitted from patient to patient but are being acquired by people before they get into the hospital, said Heidie Hornstra O’Neill, research project coordinator at MGGen.

both bacteria species can live on and in healthy people without causing any problems, one possibility is that the pathogen hangs out in people’s bodies without causing any symptoms and then proliferates when the immune systems is weakened.

It could also be that only certain strains of the bacteria cause disease while others do not. About a third of people carry Staph bacteria, for example, but only a small percentage of people get a Staph infection, which could mean only some strains are dangerous, said Paul Keim, lab director at MGGen.

The researchers are collecting demographic information as well to see if a person’s gender, ethnicity or access to healthcare plays a role in whether they carry the bacteria.


DOG POO SAMPLES:   Another potential source of C. diff bacteria, especially in a place like Flagstaff, is dogs, said Nate Stone, a research specialist at MGGen. Stone searched the sidewalks of Flagstaff for four months in the fall of 2014, collecting samples of dog poop to test them for C. diff. He found the bacteria were present in 17 percent of the 200 samples and half of the strains found are common in human C. diff infections. 

“We don’t know if dogs are giving humans C. diff or humans are giving dogs C. diff, but we do know dogs are carrying C. diff strains that can cause infections in humans, so they are probably one part of the story,” Stone said.

Next up, he’ll use genetic analysis to see if any bacteria from the dog poop samples match human samples, suggesting direct transmission.

Another possible C. diff reservoir is meat, and that’s also on Stone’s future research agenda.

The end goal of providing more data on these infection-causing bacteria is to help everyone from ordinary citizens to medical organizations figure out better ways to prevent them, Stone and Keim said.

“The reservoir stuff is fascinating because we think we can affect the way people live,” Keim said.


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U.Va.’s Division of Infectious Diseases and International Health Could Lead To a New Treatment For C. diff. Infection (CDI)



Every year, about half a million patients are infected by Clostridium difficile, an otherwise harmless bacterium that can multiply out of control when the use of antibiotics upsets the balance of microorganisms in the gut. In 2011, about 15,000 deaths were directly attributable to the infection, according to a recent study by the federal Centers for Disease Control and Prevention (CDC).

Current probiotic treatments, which promote the growth of helpful bacteria, have been ineffective against the infection, also known as C. diff.

But work being done at U.Va.’s Division of Infectious Diseases and International Health could lead to a new treatment by the end of the calendar year, according to Dr. Bill Petri, chief of the division. That’s an unusually optimistic estimate in medical research, where scientific breakthroughs predate new treatments by several years.

“Some of these advanced probiotics are actually being tested today in the clinic for their role,” Petri said. “We’re actually participating in advanced clinical trials at U.Va.”

Immunologist Erica L. Buonomo was the driving force behind the new discovery, Petri said, which has to do with the role of white blood cells in protecting against C. diff.

Buonomo found that a particular type of white blood cells, called eosinophils, act as a barrier against the infection, which breaks down the lining of the gut. These eosinophils are recruited by a protein called IL-25. A serious C. diff infection kills eosinophils, allowing the bacteria to enter the gut.

The researchers found that gut bacteria stimulate the production of IL-25, so the right probiotic could help with the production of protective eosinophils.

“We identified a pathway in the immune response that reduces the severity of an infection,” Buonomo said. “When we activate this pathway, we find mice are a lot less sick.”

The discovery would be especially helpful for elderly patients, who are most at risk. It also could have larger implications in the world of microbiology.

Eosinophils are best known for their role in allergic reactions and asthma attacks, when a high number of eosinophils cause inflammation.

The function of these cells was not entirely clear before Buonomo’s discovery. She believes this knowledge could help doctors fight other types of gastrointestinal disorders, such as irritable bowel syndrome.

U.Va. is now working on a probiotic with a Boston-based firm called Seres Therapeutics 

The finished product will be tested in Charlottesville, Petri said.

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The United States Adopted Names Council (USAN) Of the American Medical Association Has Approved the Use Of “ribaxamase” For Synthetic Biologics’ SYN-004 For the Prevention Of C. difficile Infection (CDI)


The United States Adopted Names Council (USAN) of the American Medical Association has approved the use of “ribaxamase” (Rye-bak’-sa-mase) for Synthetic Biologics’ SYN-004.

Ribaxamase is the Company’s Phase 2 development candidate designed to protect the gut microbiome from the unintended effects of certain commonly used intravenous (IV) beta-lactam antibiotics for the prevention of C. difficile infection (CDI), antibiotic-associated diarrhea (AAD) and the emergence of antibiotic-resistant organisms.

Synthetic Biologics recently reported positive results from two Phase 2a clinical trials demonstrating a correlation of the 150 mg dose of ribaxamase with the degradation of residual IV ceftriaxone alone, and in the presence of the proton pump inhibitor (PPI), esomeprazole, to levels that were near or below detectable in the intestinal chyme of healthy participants with functioning ileostomies. A Phase 2b proof-of-concept, randomized, placebo-controlled clinical trial is currently underway to evaluate the ability of ribaxamase to prevent CDI and AAD in patients hospitalized with a lower respiratory tract infection and receiving IV ceftriaxone. An interim analysis of blinded data performed by an independent data monitoring committee is expected in summer of 2016.

“The approval of the generic name ribaxamase for SYN-004 by USAN is a defining milestone for Synthetic Biologics. Ribaxamase represents a newly created and innovative first-in-class drug designed to protect the naturally occurring gut microbiome from the unintended consequences of antibiotic use,” said Jeffrey Riley, President and Chief Executive Officer. “By degrading certain IV beta-lactam antibiotics before they reach the gastrointestinal (GI) tract, ribaxamase may not only prevent the onset of CDI and AAD, but has the potential to be an instrumental tool for preventing the emergence of antibiotic resistance in organisms which comprise the gut microbiome. We are excited for the continued clinical development of ribaxamase and look forward to sharing our progress including announcing results from our ongoing global Phase 2b proof-of-concept clinical trial.”


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Clostridium difficile Research and Development Community; October 2014

Here’s the latest from the Clostridium difficile research community:
The role of hosts gut microbiome plays a critical role in the development of Clostridium difficile infection. Different antibiotic usage leads to the loss of specific bacterial taxa that can lead to different levels of susceptibility to C. difficile. In this study, Buffie et al. report that          Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to CDI which is dependent on secondary bile salts. The major take-home message is that microbiome research can help in identifying potential risks following specific antibiotic treatment and also treatment options such as probiotics.

In the following study, the authors evaluate the safety and rate of resolution of diarrhea following oral FMT with frozen capsules given to patient volunteers with recurrent CDI. Twenty patients received 15 capsules on 2 consecutive days and these patients were followed for 6 months. No SAEs were reported. Diarrhea was resolved in 14 patients following 1 FMT. 4 out of 6 nonresponders resolved after a second FMT, with an overall 90% resolution rate. Larger studies are needed to confirm the current findings.


The use of synthetic polymers as mimics of host-defense antibacterial peptides have been studied by the McBride lab. In vitro analysis of Nylon 3 copolymers against C.difficile shows that peptide LL37 is capable of blocking vegetative cell-growth and inhibiting spore outgrowth and is effective against ribotype 027 and 012 strains, in contrast to vancomycin and nisin. These easy to produce synthetic polymers could be used as a treatment for a CDI.


The following study looks at the role of IL22 and CD160 in the mucosal inflammatory immune response to a CDI. The authors report that in C. difficile-infected mice treated with anti-IL22, anti-CD160 or a combination of the two, STAT3 phosphorylation was significantly reduced compared to infected mice not receieving these antibodies. These treated mice also had reduced influx in neutrophils. These data show that IL22 and CD160 are responsible for a proinflammatory host mucosal response against during CDI in mice.

And lastly, Norway rats (Rattus norvegicus) also known as New York City rats have been found to be widely infected with many common human pathogens such as atypical enteropathogenic Escherichia coli, Clostridium difficile, and Salmonella enterica, as well as infectious agents that have been associated with undifferentiated febrile illnesses, including Bartonella spp., Streptobacillus moniliformis, Leptospira interrogans, and Seoul hantavirus and viruses such as sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses. Pest control is doubly important in urban settings where these rodents are carriers of such zoonotic diseases and live in close proximity to humans.


Chandrabali Ghose-Paul,MS,PhD, Chairperson of Research and Development

Clostridium difficile Research and Development Community – September 2014


Here is the latest from the                              Clostridium difficile research community:

The role of host factors especially those involved in the intestinal inflammatory response and pathogenesis of against Clostridium difficile is not well understood. Trindade et all looked at the role of leukotrienes in modulating host susceptibility to CDI in C57BL/6 mice. Leukotrienes are proinflammatory lipid mediators which are not involved in the pathogenesis of CDI.


Scientists from Dr. Rupnik’s group in Slovenia describe the sequence diversity of 16S-23S rRNA intergenic spacer region of 43 C difficile strains representing different PCR ribotypes. Her groups suggests that homologous recombination as a possible mechanism responsible for the evolution of 16S-23S rRNA intergenic spacer region. Diversity in sequence length, the presence or absence of different sequence modules; tRNAAla genes and different combinations of spacers of different lengths (33 bp, 53 bp or 20 bp) and 9 bp direct repeats separating the spacers could be used to describe 22 different structural groups.


The use of the bacterial second messenger cyclic di-GMP (c-di-GMP) as an adjuvant to stimulate inflammation by initiating innate immune cell recruitment and triggering the release of pro-inflammatory cytokines and chemokines was studied in the context of a C.difficile toxin expressed from an adenovirus vaccine. Although co-expression of the cyclic di-GMP via an Ad5 vector expressing diguanylate cyclase lead to modest imcrease in T cell responses, antibody titers were not boosted.



Lipotechoic acids (LTA) are novel targets for vaccination against C.difficile. LTA is expressed on spores as well as vegetative cells. In this study, the authors report on the isolation fo 5 LTAs from C. difficile as a microheterogenous mixture, differing in size and composition, structure–activity relationship studies impossible. The authors describe the synthesis of these LTAs and their functions.


The microbiome of the infant gut is established very early following birth. In this study the authors report on the resistome of the infant gut consists of aminoglycoside and β-lactam resistance reservoir even in the absence of pathogens that could provide the needed evolutionary pressure. The resistome of the infant gut is also established very early in the life of the infant, probably at birth.


Chandrabali Ghose-Paul,MS,PhD, Chairperson of Research and Development


Clostridium difficile Research and Development Community August 2014


Here’s the latest from the

Clostridium difficile Research Community:


Scientists at the University of Leicester have identified a rapid method of identifying C.difficile based on volatile organic compounds (VOCs) emitted by different C.difficile strains using Proton transfer reaction–time of flight–mass spectrometry (PTR–ToF–MS). Current methods of detecting and diagnosing CDI take anywhere between 2-5 days, leading to a delay in treatment that could have potential life threatening implications in some patients. PTR–ToF–MS analysis is capable of detecting VOCs of C.difficile metabolites in cultures within minutes and could potentially be used to detect VOCs in fecal samples from CDI patients.

CRISPR/Cas system is a form of bacterial adaptive immunity that helps control phage infections. Multiple CRISPR/Cas arrays have been identified in C.difficile. In this artciel by Hargreaves et al. the distribution and diversity of the CRISPRs have been studied and how these affect phage predation, evolution and pathogenecity.

C. difficile express flagella as a mechanism for motility, although the role of flagella in the pathogenecity of CDI is not clearly understood. Faulds-Pain et al have studied the post-translational modification of flagellin in C. difficile 630 using NMR and have identified 4 gene modification locus. Mutants strains had some impact on motility, colonization, and recurrence in a murine model of CDI showing that alterations in the flagellar structure can play a significant role in disease.

A history of C.difficile from the beginning to where we are today.


Chandrabali Ghose-Paul,MS,PhD, Chairperson of Research and Development